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1.
J Biol Chem ; 299(5): 104675, 2023 05.
Article in English | MEDLINE | ID: mdl-37028761

ABSTRACT

MafA and c-Maf are close members of the Maf transcription factor family and indicators of poor prognosis of multiple myeloma (MM). Our previous study finds that the ubiquitin ligase HERC4 induces c-Maf degradation but stabilizes MafA, and the mechanism is elusive. In the present study, we find that HERC4 interacts with MafA and mediates its K63-linked polyubiquitination at K33. Moreover, HERC4 inhibits MafA phosphorylation and its transcriptional activity triggered by glycogen synthase kinase 3ß (GSK3ß). The K33R MafA variant prevents HERC4 from inhibiting MafA phosphorylation and increases MafA transcriptional activity. Further analyses reveal that MafA can also activate the STAT3 signaling, but it is suppressed by HERC4. Lastly, we demonstrate that lithium chloride, a GSK3ß inhibitor, can upregulate HERC4 and synergizes dexamethasone, a typical anti-MM drug, in inhibiting MM cell proliferation and xenograft growth in nude mice. These findings thus highlight a novel regulation of MafA oncogenic activity in MM and provide the rationale by targeting HERC4/GSK3ß/MafA for the treatment of MM.


Subject(s)
Glycogen Synthase Kinase 3 beta , Maf Transcription Factors, Large , Multiple Myeloma , Polyubiquitin , Ubiquitin-Protein Ligases , Ubiquitination , Animals , Humans , Mice , Cell Proliferation , Dexamethasone/pharmacology , Glycogen Synthase Kinase 3 beta/metabolism , Lithium Chloride/pharmacology , Maf Transcription Factors, Large/antagonists & inhibitors , Maf Transcription Factors, Large/metabolism , Mice, Nude , Multiple Myeloma/drug therapy , Multiple Myeloma/genetics , Multiple Myeloma/metabolism , Phosphorylation , Polyubiquitin/metabolism , STAT3 Transcription Factor/metabolism , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/metabolism , Xenograft Model Antitumor Assays
2.
J Biol Chem ; 298(9): 102314, 2022 09.
Article in English | MEDLINE | ID: mdl-35926709

ABSTRACT

The zinc finger ubiquitin ligase RNF6 has been proposed as a potential therapeutic target in several cancers, but understanding its molecular mechanism of degradation has been elusive. In the present study, we find that RNF6 is degraded via auto-ubiquitination in a manner dependent on its Really Interesting New Gene (RING) domain. We determine that when the RING domain is deleted (ΔRING) or the core cysteine residues in the zinc finger are mutated (C632S/C635S), the WT protein, but not the ΔRING or mutant RNF6 protein, undergoes polyubiquitination. We also identify USP7 as a deubiquitinase of RNF6 by tandem mass spectrometry. We show that USP7 interacts with RNF6 and abolishes its K48-linked polyubiquitination, thereby preventing its degradation. In contrast, we found a USP7-specific inhibitor promotes RNF6 polyubiquitination, degradation, and cell death. Furthermore, we demonstrate the anti-leukemic drug Nilotinib and anti-myeloma drug Panobinostat (LBH589) induce RNF6 K48-linked polyubiquitination and degradation in both multiple myeloma (MM) and leukemia cells. In agreement with our hypothesis on the mode of RNF6 degradation, we show these drugs promote RNF6 auto-ubiquitination in an in vitro ubiquitination system without other E3 ligases. Consistently, reexpression of RNF6 ablates drug-induced MM and leukemia cell apoptosis. Therefore, our results reveal that RNF6 is a RING E3 ligase that undergoes auto-ubiquitination, which could be abolished by USP7 and induced by anti-cancer drugs. We propose that chemical induction of RNF6 auto-ubiquitination and degradation could be a novel strategy for the treatment of hematological malignancies including MM and leukemia.


Subject(s)
Antineoplastic Agents , DNA-Binding Proteins , Leukemia, Myelogenous, Chronic, BCR-ABL Positive , Multiple Myeloma , Panobinostat , Ubiquitin-Protein Ligases , Ubiquitination , Zinc Fingers , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Cysteine/metabolism , DNA-Binding Proteins/metabolism , Humans , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , Multiple Myeloma/drug therapy , Panobinostat/pharmacology , Panobinostat/therapeutic use , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Specific Peptidase 7/metabolism
3.
Blood ; 137(11): 1478-1490, 2021 03 18.
Article in English | MEDLINE | ID: mdl-32842143

ABSTRACT

The oncogenic transcription factor c-Maf has been proposed as an ideal therapeutic target for multiple myeloma (MM), but how to achieve it is still elusive. In the present study, we found the Otub1/c-Maf axis could be a potential target. Otub1, an OTU family deubiquitinase, was found to interact with c-Maf by mass spectrometry. Otub1 abrogates c-Maf K48-linked polyubiquitination, thus preventing its degradation and enhancing its transcriptional activity. Specifically, this deubiquitinating activity depends on its Lys71 and the N terminus but is independent of UBE2O, a known E2 of c-Maf. Otub1 promotes MM cell survival and MM tumor growth. In contrast, silence of Otub1 leads to c-Maf degradation and c-Maf-expressing MM cell apoptosis. Therefore, the Otub1/c-Maf axis could be a therapeutic target of MM. In order to explore this concept, we performed a c-Maf recognition element-driven luciferase-based screen against US Food and Drug Administration-approved drugs and natural products, from which the generic cardiac glycoside lanatoside C (LanC) is found to prevent c-Maf deubiquitination and induces its degradation by disrupting the interaction of Otub1 and c-Maf. Consequently, LanC inhibits c-Maf transcriptional activity, induces c-Maf-expressing MM cell apoptosis, and suppresses MM growth and prolongs overall survival of model mice, but without apparent toxicity. Therefore, the present study identifies Otub1 as a novel deubiquitinase of c-Maf and establishes that the Otub1/c-Maf axis is a potential therapeutic target for MM.


Subject(s)
Antineoplastic Agents/pharmacology , Deubiquitinating Enzymes/metabolism , Multiple Myeloma/drug therapy , Protein Interaction Maps/drug effects , Proto-Oncogene Proteins c-maf/metabolism , Animals , Antineoplastic Agents/therapeutic use , Cell Line, Tumor , Drug Discovery , HEK293 Cells , Humans , Mice, Inbred BALB C , Mice, Nude , Multiple Myeloma/metabolism , Signal Transduction/drug effects , Ubiquitination/drug effects
4.
Biomacromolecules ; 24(12): 5871-5883, 2023 12 11.
Article in English | MEDLINE | ID: mdl-37788665

ABSTRACT

Fibrillar collagen is the major protein in the extracellular matrix and regulates cell behavior via chemical and mechanical cues. The key structural element of collagen fibrils is the axially repeating D-period, formed by the lateral association of collagen triple helices. We have developed fibril-forming collagen mimetic peptides (FCMPs) with repeated amino acid sequences, which form fibrils having D-period-like structures. Containing over 100 amino acid residues, these peptides are produced by bacterial expression using designed genes. Here, we report the fibrillogenesis of a new FCMP containing an α-helix coiled coil domain. The latest findings highlight the importance of the amino acid sequence periodicity in FCMP fibril formation. Additionally, our results demonstrate the remarkable adaptability of collagen fibrils' molecular packing. Mirroring native collagen fibrils, in both the structure and the fibrillogenesis process, these FCMPs are useful molecular tools for advancing collagen research and developing novel biomaterials.


Subject(s)
Collagen , Peptides , Collagen/chemistry , Peptides/chemistry , Amino Acid Sequence , Protein Conformation, alpha-Helical , Protein Domains
5.
Acta Pharmacol Sin ; 44(9): 1920-1931, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37055530

ABSTRACT

The cell cycle regulator cyclin D3 (CCND3) is highly expressed in multiple myeloma (MM) and it promotes MM cell proliferation. After a certain phase of cell cycle, CCND3 is rapidly degraded, which is essential for the strict control of MM cell cycle progress and proliferation. In the present study, we investigated the molecular mechanisms regulating CCND3 degradation in MM cells. By utilizing affinity purification-coupled tandem mass spectrometry, we identified the deubiquitinase USP10 interacting with CCND3 in human MM OPM2 and KMS11 cell lines. Furthermore, USP10 specifically prevented CCND3 from K48-linked polyubiquitination and proteasomal degradation, therefore enhancing its activity. We demonstrated that the N-terminal domain (aa. 1-205) of USP10 was dispensable for binding to and deubiquitinating CCND3. Although Thr283 was important for CCND3 activity, it was dispensable for CCND3 ubiquitination and stability modulated by USP10. By stabilizing CCND3, USP10 activated the CCND3/CDK4/6 signaling pathway, phosphorylated Rb, and upregulated CDK4, CDK6 and E2F-1 in OPM2 and KMS11 cells. Consistent with these findings, inhibition of USP10 by Spautin-1 resulted in accumulation of CCND3 with K48-linked polyubiquitination and degradation that synergized with Palbociclib, a CDK4/6 inhibitor, to induce MM cell apoptosis. In nude mice bearing myeloma xenografts with OPM2 and KMS11 cells, combined administration of Spautin-l and Palbociclib almost suppressed tumor growth within 30 days. This study thus identifies USP10 as the first deubiquitinase of CCND3 and also finds that targeting the USP10/CCND3/CDK4/6 axis may be a novel modality for the treatment of myeloma.


Subject(s)
Multiple Myeloma , Mice , Animals , Humans , Cyclin D3 , Multiple Myeloma/metabolism , Mice, Nude , Apoptosis , Deubiquitinating Enzymes , Cell Line, Tumor , Ubiquitin Thiolesterase/metabolism
6.
Subcell Biochem ; 99: 495-521, 2022.
Article in English | MEDLINE | ID: mdl-36151387

ABSTRACT

The diverse and complex functions of collagen during the development of an organism are closely related to the polymorphism of its supramolecular structures in the extracellular matrix. SLS (segment-long-spacing) is one of the best understood alternative structures of collagen. SLS played an instrumental role in the original studies of collagen more than half a century ago that laid the foundation of nearly everything we know about collagen today. Despite being used mostly under in vitro conditions, the natural occurrence of SLS in tissues has also been reported. Here we will provide a brief overview of the major findings of the SLS and other structures of collagen based on a wealth of work published starting from the 1940s. We will discuss the factors that determine the stability and the structural specificity of the different molecular assemblies of collagen in light of the new studies using designed fibril forming collagen peptides. At the end of the chapter, we will summarize some recent discoveries of the alternative structures of collagen in tissues, especially those involved in pathogenic states. A revisit of SLS will likely inspire new understandings concerning the range of critical roles of fibrillar collagen in terms of its organizational diversity in the extracellular matrix.


Subject(s)
Collagen , Fibrillar Collagens , Collagen/chemistry , Extracellular Matrix , Fibrillar Collagens/chemistry
7.
Crit Rev Food Sci Nutr ; : 1-15, 2022 Nov 15.
Article in English | MEDLINE | ID: mdl-36377729

ABSTRACT

Enterohemorrhagic Escherichia coli is considered one of the primary bacterial pathogens that cause foodborne diseases because it can survive in meat, vegetables and so on. Understanding of the effect of vegetable characteristics on the adhesion and proliferation process of EHEC is necessary to develop control measures. In this review, the amount and methods of adhesion, the internalization pathway and proliferation process of EHEC have been described during the vegetable contamination. Types, cultivars, tissue characteristics, leaf age, and damage degree can affect EHEC adhesion on vegetables. EHEC cells contaminate the root surface of vegetables through soil and further internalize. It can also contaminate the stem scar tissue of vegetables by rain or irrigation water and internalize the vertical axis, as well as the stomata, necrotic lesions and damaged tissues of vegetable leaves. After EHEC adhered to the vegetables, they may further proliferate and form biofilms. Leaf and fruit tissues were more sensitive to biofilm formation, and shedding rate of biofilms on epidermis tissue was faster. Insights into the mechanisms of vegetable contamination by EHEC, including the role of exopolysaccharides and proteins responsible for movement, adhesion and oxidative stress response could reveal the molecular mechanism by which EHEC contaminates vegetables.

8.
Mol Biol Rep ; 49(1): 451-461, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34731371

ABSTRACT

BACKGROUND: Sulforaphane (SFN) is a kind of isothiocyanate from cruciferous vegetables with extensive anti-tumor activity. Esophageal squamous cell carcinoma (ESCC) is a popular malignancy in East Asia, East and South Africa, while the more efficient medicines and therapeutic strategies are still lack. This study aims to explore the anti-tumor activity of SFN alone and combined with Akt/mTOR pathway inhibitors as well as the potential molecular mechanism in ESCC. METHODS AND RESULTS: Cell proliferation, migration, cell cycle phase, apoptosis and protein expression were detected with MTT assay, clone formation experiment, wound healing assays, flow cytometry and Western blot, respectively, after ESCC cells ECa109 and EC9706 treated with SFN alone or combined with Akt/mTOR inhibitors. Xenograft models were used to evaluate the efficiency and mechanism of SFN combined with PP242 in vivo. The results showed that SFN significantly inhibited the viability and induced apoptosis of ECa109 and EC9706 cells by increasing expression of Cleaved-caspase 9. SFN combined with PP242, but not MK2206 and RAD001, synergetic inhibited proliferation of ESCC cells. Moreover, compared to SFN alone, combination of SFN and PP242 had stronger inhibiting efficiency on clone formation, cell migratory, cell cycle phase and growth of xenografts, as well as the more powerful apoptosis-inducing effects on ESCC. The mechanism was that PP242 abrogated the promoting effects of SFN on p-p70S6K (Thr389) and p-Akt (Ser473) in ESCC. CONCLUSIONS: Our findings demonstrate that PP242 enhances the anti-tumor activity of SFN by blocking SFN-induced activation of Akt/mTOR pathway in ESCC, which provides a rationale for treating ESCC using SFN combined with Akt/mTOR pathway inhibitors.


Subject(s)
Indoles/pharmacology , Isothiocyanates/pharmacology , MTOR Inhibitors/pharmacology , Proto-Oncogene Proteins c-akt/metabolism , Purines/pharmacology , Signal Transduction/drug effects , Sulfoxides/pharmacology , TOR Serine-Threonine Kinases/antagonists & inhibitors , Animals , Cell Line, Tumor , Disease Models, Animal , Drug Synergism , Esophageal Neoplasms , Humans , Immunophenotyping , Mice , Models, Biological , Xenograft Model Antitumor Assays
9.
Appl Microbiol Biotechnol ; 106(18): 6181-6194, 2022 Sep.
Article in English | MEDLINE | ID: mdl-35962282

ABSTRACT

Probiotics have the potential to be used in the prevention of Clostridioides difficile infection (CDI). In this study, selenium (Se)-enriched Bifidobacterium breve YH68-Se was obtained under optimal culture conditions with single-factor and response surface optimization. The overall environmental resistance of YH68-Se was superior to that of the parental strain YH68, mainly reflected in the substantial improvement of antioxidant activity and gastrointestinal tolerance. YH68-Se dramatically inhibited C. difficile growth, spore, biofilm, toxin production, and virulence gene expression, rapidly disrupted C. difficile cell membrane permeability and integrity, and altered the membrane proton motive force (PMF), induced a large outflow of intracellular substances and eventually caused bacterial death. The main factor inducing this process originated from the lactic acid (LD) in YH68-Se. In addition, the LD production of YH68 increased with increasing selenite concentration and was accompanied by enhanced activities of thioredoxin reductase (TrxR), glutathione peroxidase (GSH-Px), and increased concentration of autoinducer-2 (AI-2), which may be the crucial factors contributing to the outstanding probiotic properties of YH68-Se and their potent antagonism of C. difficile. KEY POINTS: • Compared with the parental strain B. breve YH68, the environmental resistance of YH68-Se was improved. • YH68-Se was able to produce more lactic acid, which suppressed the important physiological activities of C. difficile and rapidly disrupted their cell membrane structures. • Sodium selenite in the suitable concentration range gradually increases the yield of lactic acid and phenylacetic acid, increased the concentration of autoinducer-2, and enhanced the activities of antioxidant enzymes TrxR and GSH-Px in YH68.


Subject(s)
Bifidobacterium breve , Clostridioides difficile , Selenium , Antioxidants , Bifidobacterium breve/metabolism , Clostridioides , Glutathione Peroxidase/metabolism , Lactic Acid , Selenium/metabolism
10.
Sensors (Basel) ; 22(6)2022 Mar 15.
Article in English | MEDLINE | ID: mdl-35336432

ABSTRACT

Deep learning techniques are the future trend for designing heart sound classification methods, making conventional heart sound segmentation dispensable. However, despite using fixed signal duration for training, no study has assessed its effect on the final performance in detail. Therefore, this study aims at analysing the duration effect on the commonly used deep learning methods to provide insight for future studies in data processing, classifier, and feature selection. The results of this study revealed that (1) very short heart sound signal duration (1 s) weakens the performance of Recurrent Neural Networks (RNNs), whereas no apparent decrease in the tested Convolutional Neural Network (CNN) model was found. (2) RNN outperformed CNN using Mel-frequency cepstrum coefficients (MFCCs) as features. There was no difference between RNN models (LSTM, BiLSTM, GRU, or BiGRU). (3) Adding dynamic information (∆ and ∆²MFCCs) of the heart sound as a feature did not improve the RNNs' performance, and the improvement on CNN was also minimal (≤2.5% in MAcc). The findings provided a theoretical basis for further heart sound classification using deep learning techniques when selecting the input length.


Subject(s)
Deep Learning , Heart Sounds , Neural Networks, Computer
11.
J Biol Chem ; 295(7): 2084-2096, 2020 02 14.
Article in English | MEDLINE | ID: mdl-31822558

ABSTRACT

The Maf proteins, including c-Maf, MafA, and MafB, are critical transcription factors in myelomagenesis. Previous studies demonstrated that Maf proteins are processed by the ubiquitin-proteasome pathway, but the mechanisms remain elusive. This study applied MS to identify MafB ubiquitination-associated proteins and found that the ubiquitin-specific protease USP7 was present in the MafB interactome. Moreover, USP7 also interacted with c-Maf and MafA and blocked their polyubiquitination and degradation. Consistently, knockdown of USP7 resulted in Maf protein degradation along with increased polyubiquitination levels. The action of USP7 thus promoted Maf transcriptional activity as evidenced by luciferase assays and by the up-regulation of the expression of Maf-modulated genes. Furthermore, USP7 was up-regulated in myeloma cells, and it was negatively associated with the survival of myeloma patients. USP7 promoted myeloma cell survival, and when it was inhibited by its specific inhibitor P5091, myeloma cell lines underwent apoptosis. These results therefore demonstrated that USP7 is a deubiquitinase of Maf proteins and promotes MM cell survival in association with Maf stability. Given the significance of USP7 and Maf proteins in myeloma genesis, targeting the USP7/Maf axle is a potential strategy to the precision therapy of MM.


Subject(s)
Maf Transcription Factors, Large/genetics , MafB Transcription Factor/genetics , Multiple Myeloma/genetics , Proto-Oncogene Proteins c-maf/genetics , Ubiquitin-Specific Peptidase 7/genetics , Apoptosis/drug effects , Carcinogenesis/genetics , Cell Proliferation/genetics , Cell Survival/genetics , Female , Gene Expression Regulation, Neoplastic/drug effects , HEK293 Cells , Humans , Male , Multiple Myeloma/pathology , Polyubiquitin/genetics , Progression-Free Survival , Proteolysis/drug effects , Thiophenes/pharmacology , Ubiquitin-Specific Peptidase 7/antagonists & inhibitors , Ubiquitination/genetics
12.
Cell Commun Signal ; 19(1): 24, 2021 02 24.
Article in English | MEDLINE | ID: mdl-33627137

ABSTRACT

BACKGROUND: The oncogenic transcript factor c-Maf is stabilized by the deubiquitinase Otub1 and promotes myeloma cell proliferation and confers to chemoresistance. Inhibition of the Otub1/c-Maf axis is a promising therapeutic target, but there are no inhibitors reported on this specific axis. METHODS: A luciferase assay was applied to screen potential inhibitors of Otub1/c-Maf. Annexin V staining/flow cytometry was applied to evaluate cell apoptosis. Immunoprecipitation was applied to examine protein ubiquitination and interaction. Xenograft models in nude mice were used to evaluate anti-myeloma activity of AVT. RESULTS: Acevaltrate (AVT), isolated from Valeriana glechomifolia, was identified based on a bioactive screen against the Otub1/c-Maf/luciferase system. AVT disrupts the interaction of Otub1/c-Maf thus inhibiting Otub1 activity and leading to c-Maf polyubiquitination and subsequent degradation in proteasomes. Consistently, AVT inhibits c-Maf transcriptional activity and downregulates the expression of its target genes key for myeloma growth and survival. Moreover, AVT displays potent anti-myeloma activity by triggering myeloma cell apoptosis in vitro and impairing myeloma xenograft growth in vivo but presents no marked toxicity. CONCLUSIONS: The natural product AVT inhibits the Otub1/c-Maf axis and displays potent anti-myeloma activity. Given its great safety and efficacy, AVT could be further developed for MM treatment. Video Abstract.


Subject(s)
Antineoplastic Agents, Phytogenic/therapeutic use , Cysteine Endopeptidases/metabolism , Cysteine Proteinase Inhibitors/therapeutic use , Iridoids/therapeutic use , Multiple Myeloma/drug therapy , Proto-Oncogene Proteins c-maf/antagonists & inhibitors , Animals , Antineoplastic Agents, Phytogenic/pharmacology , Apoptosis/drug effects , Cell Line , Cell Survival/drug effects , Cysteine Endopeptidases/genetics , Cysteine Proteinase Inhibitors/pharmacology , Female , Humans , Iridoids/pharmacology , Mice, Inbred BALB C , Mice, Nude , Multiple Myeloma/metabolism , Multiple Myeloma/pathology , Proto-Oncogene Proteins c-maf/genetics , Proto-Oncogene Proteins c-maf/metabolism
13.
Acta Pharmacol Sin ; 42(8): 1338-1346, 2021 Aug.
Article in English | MEDLINE | ID: mdl-33184448

ABSTRACT

Recent studies show that the expression of CCND1, a key factor in cell cycle control, is increased following the progress and deteriotation of glioma and predicts poor outcomes. On the other hand, dysregulated deubiquitinase USP10 also predicts poor prognosis for patients with glioblastoma (GBM). In the present study, we investigated the interplay between CCND1 protein and USP10 in GBM cells. We showed that the expression of CCND1 was significantly higher in both GBM tissues and GBM-derived stem cells. USP10 interacted with CCND1 and prevented its K48- but not K63-linked polyubiquitination in GBM U251 and HS683 cells, which led to increased CCND1 stability. Consistent with the action of USP10 on CCND1, knockdown of USP10 by single-guided RNA downregulated CCND1 and caused GBM cell cycle arrest at the G1 phase and induced GBM cell apoptosis. To implement this finding in the treatment of GBMs, we screened a natural product library and found that acevaltrate (AVT), an active component derived from the herbal plant Valeriana jatamansi Jones was strikingly potent to induce GBM cell apoptosis, which was confirmed by the Annexin V staining and activation of the apoptotic signals. Furthermore, we revealed that AVT concentration-dependently suppressed USP10-mediated deubiquitination on CCND1 therefore inducing CCND1 protein degradation. Collectively, the present study demonstrates that the USP10/CCND1 axis could be a promising therapeutic target for patients with GBMs.


Subject(s)
Cyclin D1/metabolism , Glioblastoma/metabolism , Iridoids/pharmacology , Ubiquitin Thiolesterase/metabolism , Ubiquitination/physiology , Apoptosis/drug effects , Cell Line, Tumor , Cell Proliferation/physiology , Glioblastoma/drug therapy , HEK293 Cells , Humans , Ubiquitin Thiolesterase/antagonists & inhibitors , Ubiquitination/drug effects
14.
Neurocomputing (Amst) ; 443: 96-105, 2021 Jul 05.
Article in English | MEDLINE | ID: mdl-33753962

ABSTRACT

The early detection of infection is significant for the fight against the ongoing COVID-19 pandemic. Chest X-ray (CXR) imaging is an efficient screening technique via which lung infections can be detected. This paper aims to distinguish COVID-19 positive cases from the other four classes, including normal, tuberculosis (TB), bacterial pneumonia (BP), and viral pneumonia (VP), using CXR images. The existing COVID-19 classification researches have achieved some successes with deep learning techniques while sometimes lacking interpretability and generalization ability. Hence, we propose a two-stage classification method MANet to address these issues in computer-aided COVID-19 diagnosis. Particularly, a segmentation model predicts the masks for all CXR images to extract their lung regions at the first stage. A followed classification CNN at the second stage then classifies the segmented CXR images into five classes based only on the preserved lung regions. In this segment-based classification task, we propose the mask attention mechanism (MA) which uses the predicted masks at the first stage as spatial attention maps to adjust the features of the CNN at the second stage. The MA spatial attention maps for features calculate the percentage of masked pixels in their receptive fields, suppressing the feature values based on the overlapping rates between their receptive fields and the segmented lung regions. In evaluation, we segment out the lung regions of all CXR images through a UNet with ResNet backbone, and then perform classification on the segmented CXR images using four classic CNNs with or without MA, including ResNet34, ResNet50, VGG16, and Inceptionv3. The experimental results illustrate that the classification models with MA have higher classification accuracy, more stable training process, and better interpretability and generalization ability than those without MA. Among the evaluated classification models, ResNet50 with MA achieves the highest average test accuracy of 96.32 % in three runs, and the highest one is 97.06 % . Meanwhile, the attention heat maps visualized by Grad-CAM indicate that models with MA make more reliable predictions based on the pathological patterns in lung regions. This further presents the potential of MANet to provide clinicians with diagnosis assistance.

15.
Molecules ; 26(19)2021 Oct 02.
Article in English | MEDLINE | ID: mdl-34641525

ABSTRACT

2,5-diketopiperazines (DKPs) are cyclic dipeptides ubiquitously found in nature. In particular, cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) are frequently detected in many microbial cultures. Each of these DKPs has four possible stereoisomers due to the presence of two chirality centers. However, absolute configurations of natural DKPs are often ambiguous due to the lack of a simple, sensitive, and reproducible method for stereochemical assignment. This is an important problem because stereochemistry is a key determinant of biological activity. Here, we report a synthetic DKP library containing all stereoisomers of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro). The library was subjected to spectroscopic characterization using mass spectrometry, NMR, and electronic circular dichroism (ECD). It turned out that ECD can clearly differentiate DKP stereoisomers. Thus, our ECD dataset can serve as a reference for unambiguous stereochemical assignment of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) samples from natural sources. The DKP library was also subjected to a biological screening using assays for E. coli growth and biofilm formation, which revealed distinct biological effects of cyclo(D-Phe-L-Pro).


Subject(s)
Dipeptides/chemistry , Peptides, Cyclic/chemistry , Circular Dichroism , Diketopiperazines/chemistry , Dipeptides/chemical synthesis , Dipeptides/pharmacology , Escherichia coli/drug effects , Peptides, Cyclic/chemical synthesis , Peptides, Cyclic/pharmacology , Stereoisomerism , Structure-Activity Relationship
16.
J Comput Chem ; 41(10): 1026-1033, 2020 Apr 15.
Article in English | MEDLINE | ID: mdl-31970817

ABSTRACT

Metal azides have attracted increasing attention as precursors for synthesizing polymeric nitrogen. In this article, we report the amorphous polymerization of nitrogen by compressing cupric azide. The ab initio molecular dynamics simulations show that crystalline cupric azide transforms into a disordered network composed of singly bonded nitrogen at a hydrostatic pressure of 40 GPa and room temperature. The transformation manifests the formation of a π delocalization along the disordered Cu-N network, thus resulting in a semiconductor-metal transition. The estimated heat of formation of the amorphous polymeric nitrogen system is comparable to conventional high-energy-density materials. The amorphization provides an alternative route to the polymerization of nitrogen under moderate conditions.

17.
Bioconjug Chem ; 31(12): 2789-2806, 2020 12 16.
Article in English | MEDLINE | ID: mdl-33210532

ABSTRACT

Chemoselective reactions with thiols have long held promise for the site-specific bioconjugation of antibodies and antibody fragments. Yet bifunctional probes bearing monovalent maleimides-long the "gold standard" for thiol-based ligations-are hampered by two intrinsic issues: the in vivo instability of the maleimide-thiol bond and the need to permanently disrupt disulfide linkages in order to facilitate bioconjugation. Herein, we present the synthesis, characterization, and validation of DiPODS, a novel bioconjugation reagent containing a pair of oxadiazolyl methyl sulfone moieties capable of irreversibly forming covalent bonds with two thiolate groups while simultaneously rebridging disulfide linkages. The reagent was synthesized from commercially available starting materials in 8 steps, during which rotamers were encountered and investigated both experimentally and computationally. DiPODS is designed to be modular and can thus be conjugated to any payload through a pendant terminal primary amine (DiPODS-PEG4-NH2). Subsequently, the modification of a HER2-targeting Fab with a fluorescein-conjugated variant of DiPODS (DiPODS-PEG4-FITC) reinforced the site-specificity of the reagent, illustrated its ability to rebridge disulfide linkages, and produced an immunoconjugate with in vitro properties superior to those of an analogous construct created using traditional stochastic bioconjugation techniques. Ultimately, we believe that this work has particularly important implications for the synthesis of immunoconjugates, specifically for ensuring that the attachment of cargoes to immunoglobulins is robust, irreversible, and biologically and structurally benign.


Subject(s)
Disulfides/chemistry , Binding Sites , Indicators and Reagents/chemistry , Polyethylene Glycols/chemistry , Substrate Specificity , Sulfhydryl Compounds/chemistry , Sulfones/chemistry
18.
Acta Pharmacol Sin ; 41(3): 394-403, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31645658

ABSTRACT

RNF6, a RING-type ubiquitin ligase, has been identified as an oncogene in various cancers but its role in multiple myeloma (MM) remains elusive. In the present study we first showed that the expression levels of RNF6 in MM were significantly elevated compared with the bone marrow cells of healthy donors. Overexpression of RNF6 in LP1 and PRMI-8266 MM cell lines promoted cell proliferation, whereas knockdown of RNF6 led to apoptosis of MM cells. Furthermore, we revealed that RNF6, as a ubiquitin ligase, interacted with glucocorticoid receptor (GR) and induced its K63-linked polyubiquitination. Different from current knowledge, RNF6 increased GR stability at both endogenous and exogenous contexts. Such an action greatly promoted GR transcriptional activity, which was confirmed by luciferase assays and by the increased expression levels of prosurvival genes including Bcl-xL and Mcl-1, two typical downstream genes of the GR pathway. Consistent with these findings, ectopic expression of RNF6 in MM cells conferred resistance to dexamethasone, a typical anti-myeloma agent. In conclusion, we demonstrate that RNF6 promotes MM cell proliferation and survival by inducing atypical polyubiquitination to GR, and RNF6 could be a promising therapeutic target for the treatment of MM.


Subject(s)
DNA-Binding Proteins/metabolism , Multiple Myeloma/metabolism , Receptors, Glucocorticoid/metabolism , Cell Proliferation , Cell Survival , Cells, Cultured , DNA-Binding Proteins/genetics , Dose-Response Relationship, Drug , Humans , Molecular Structure , Multiple Myeloma/pathology , Receptors, Glucocorticoid/genetics , Structure-Activity Relationship , Ubiquitination
19.
An Acad Bras Cienc ; 92(4): e20191148, 2020.
Article in English | MEDLINE | ID: mdl-33237136

ABSTRACT

The current study was designed to investigate the effects and the mechanism of catalpol on myocardial ischemia-reperfusion (MI/R) injury in a diabetic rat model. Male Sprague-Dawley rats were divided into DM + sham, DM +I/R, and DM +I/R + C groups and diabetes was induced using single injections of streptozotocin (STZ; 70 mg/kg; i.p). After confirming the induction of diabetes, rats were administered physiological saline and catalpol (10 mg/kg; i.p.) daily for 28 days. Subsequently, rats were subjected to left anterior descending (LAD) coronary artery occlusion for 30 min followed by reperfusion for 2 h. Haemodynamic parameters were recorded throughout surgery, and following sacrifice, hearts were isolated for biochemical, histopathological, and molecular analyses. Catalpol treatment significantly ameliorated MI/R injury by improving cardiac function, normalizing myocardial enzyme activities and markers of oxidative stress, and by maintaining myocardial architecture. Furthermore, expression levels of the inflammatory cytokines TNF-α and IL-6 were decreased in biochemical and immunohistochemical studies. Additionally, the cardioprotective effects of catalpol were partly related to reductions in myocardial endoplasmic reticulum stress (ERS). In conclusion, catalpol exerts cardioprotective effects in diabetic rats by attenuating inflammation and inhibiting ERS.


Subject(s)
Diabetes Mellitus, Experimental , Myocardial Reperfusion Injury , Animals , Anti-Inflammatory Agents/pharmacology , Apoptosis , Diabetes Mellitus, Experimental/drug therapy , Endoplasmic Reticulum Stress , Iridoid Glucosides , Male , Myocardial Reperfusion Injury/drug therapy , Oxidative Stress , Rats , Rats, Sprague-Dawley , Streptozocin
20.
J Food Sci Technol ; 57(3): 886-894, 2020 Mar.
Article in English | MEDLINE | ID: mdl-32123409

ABSTRACT

It is an interesting topic to elucidate the interaction among plant proteins and bioactive lipid components. However, there is a shortage of understanding regarding the nature of the interaction between rice protein and conjugated linoleic acid (CLA). In this study, the intrinsic fluorescence intensity of rice glutelin (RG) was quenched upon increasing concentrations of CLA, indicating the occurrence of an interaction between them. Thermodynamic analysis showed that the RG-CLA binding process occurred spontaneously and hydrogen bonds were the primary driving force. Moreover, only one binding site was calculated between RG and CLA by the intrinsic fluorescence data. The surface hydrophobicity of RG was reduced with increasing CLA. Circular dichroism and synchronous fluorescence spectroscopy showed conformational and microenvironmental changes around the chromophores of RG. The α-helical content increased and ß-sheet content declined after the binding reaction. The computational docking program displayed the target site in which CLA and amino acid residues of RG might be linked together. This study provides valuable insights into the nature of the interactions between plant proteins and fatty acids.

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